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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Create recipe for medaka 1.12.0 please #48855

Closed ZarulHanifah closed 2 weeks ago

ZarulHanifah commented 3 months ago

"Oxford Nanopore Technologies does not supply or support the bioconda distribution of medaka. Please raise this issue on the bioconda issues page."

Idk why wouldnt ONT put their own software on bioconda for easy distribution. Anyways, please help me! The pip link is here: https://pypi.org/project/medaka/

aliciaaevans commented 3 months ago

I'm rebuilding https://github.com/bioconda/bioconda-recipes/pull/48523 to see what errors might be keeping the update from being merged.

martin-g commented 3 months ago

The problem is here - https://github.com/bioconda/bioconda-recipes/blob/d9a796700d865402b03bccf5b2081f22b35eb1ef/recipes/medaka/conda_build_config.yaml Medaka uses tensorflow 2.10 (https://github.com/nanoporetech/medaka/blob/0cc6f51c96f47eaf8f2135c3082980d0e7f75494/requirements.txt#L8) that needs OpenSSL 1.1.1 but Medaka itself needs OpenSSL 3.x The "fix" is easy - https://github.com/bioconda/bioconda-recipes/pull/46801/files#diff-c4e50da4c5af49617da084e58a8fe2bd721475988e0cd0b8c8ffa4900c430be8. But I am not sure whether it will cause problems at runtime later.

martin-g commented 3 months ago 
09:23:21 BIOCONDA INFO (OUT) Encountered problems while solving:
09:23:21 BIOCONDA INFO (OUT)   - package htslib-1.14-h9093b5e_0 requires libcurl >=7.79.1,<8.0a0, but none of the providers can be installed
09:23:21 BIOCONDA INFO (OUT) 
09:23:21 BIOCONDA INFO (OUT) Could not solve for environment specs
09:23:21 BIOCONDA INFO (OUT) The following packages are incompatible
09:23:21 BIOCONDA INFO (OUT) ├─ htslib >=1.14  is installable with the potential options
09:23:21 BIOCONDA INFO (OUT) │  ├─ htslib [1.14|1.15] would require
09:23:21 BIOCONDA INFO (OUT) │  │  └─ libcurl >=7.81.0,<8.0a0 , which can be installed;
09:23:21 BIOCONDA INFO (OUT) │  ├─ htslib 1.14 would require
09:23:21 BIOCONDA INFO (OUT) │  │  └─ libcurl >=7.79.1,<8.0a0 , which can be installed;
09:23:21 BIOCONDA INFO (OUT) │  ├─ htslib [1.15.1|1.16] would require
09:23:21 BIOCONDA INFO (OUT) │  │  └─ libcurl >=7.83.1,<8.0a0 , which can be installed;
09:23:21 BIOCONDA INFO (OUT) │  ├─ htslib 1.15.1 would require
09:23:21 BIOCONDA INFO (OUT) │  └─ libcurl 8.8.0, which can be installed (as previously explained);
09:23:21 BIOCONDA INFO (OUT) └─ openssl 1.1.1.*  is not installable because it conflicts with any installable versions previously reported.
09:23:28 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmp2f3wwsrm/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld:/opt/host-conda-bld -v /home/vsts/work/1/s/recipes/medaka:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:3.3.1 /bin/bash /opt/build_script.bash
ZarulHanifah commented 3 months ago

I can try runtime and see if it works